.
The Open Protein Structure Annotation Network
PDB Keyword
.

3ky8

    Table of contents
    1. 1. Protein Summary
    2. 2.
      1. 2.1. Ligand Summary

    Title Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3ky8 Target Id
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS29509,YP_001092907.1, _0023.002889_, 326351
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 2
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.30 Rfactor 0.181
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 46.60

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3ky8
    1. Characterisation of an oxidoreductase from the Arylamine N_acetyltransferase operon in Mycobacterium smegmatis
    D Evangelopoulos, N Cronin, T Daviter, E Sim - FEBS , 2011 - Wiley Online Library
     

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    Pfam update: RibD_C (PF01872) family

    394242 from Shewanella sp. pv-4 encodes a protein which belongs to Pfam; PF01872; RibD_C; thought to be involved in riboflavin biosynthesis.

    There are two protomers (A and B chains; biological dimer) found in the asu.

    asu.png

    Figure 1. Two protomers in asu.

     


     

    The PDB hits of structural homologs by DALI are:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 1cz3-B 19.5 2.1 160 168 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 2: 1d1g-B 19.4 2.2 159 165 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 3: 1cz3-A 19.3 2.2 159 164 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 4: 1d1g-A 19.2 2.2 159 165 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 5: 2gd9-B 18.0 2.3 153 171 25 PDB MOLECULE: HYPOTHETICAL PROTEIN YYAP; 6: 2azn-F 17.8 2.3 166 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 7: 2azn-C 17.8 2.2 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 8: 2azn-B 17.8 2.2 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 9: 2azn-A 17.7 2.3 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 10: 2azn-E 17.7 2.3 166 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 11: 2azn-D 17.7 2.3 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 12: 2gd9-A 17.2 2.3 152 177 25 PDB MOLECULE: HYPOTHETICAL PROTEIN YYAP; 13: 3ex8-B 17.1 2.5 168 359 17 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 14: 2d5n-D 17.1 2.4 168 360 18 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 15: 2d5n-C 17.1 2.5 169 359 18 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 16: 2b3z-D 17.0 2.4 165 360 18 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 17: 2hxv-A 17.0 2.5 164 349 18 PDB MOLECULE: DIAMINOHYDROXYPHOSPHORIBOSYLAMINOPYRIMIDINE 18: 3ex8-D 17.0 2.5 168 360 17 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 19: 3dl6-B 16.3 2.5 156 510 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 20: 2oip-B 16.2 2.4 156 516 15 PDB MOLECULE: CHAIN A, CRYSTAL STRUCTURE OF DHFR; 21: 3dl5-A 16.2 2.5 154 509 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 22: 3dl5-D 16.2 2.6 156 509 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 23: 3dl6-A 16.2 2.6 155 507 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 24: 3dl5-B 16.2 2.6 156 510 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 25: 1vdr-A 16.2 2.5 152 157 16 PDB MOLECULE: DIHYDROFOLATE REDUCTASE;

     

    Superposition of the 394242 with 1d1g shows that their active site resides are conserved. Interestingly, there are two UNLs bound in the each protomer of 394242. UNL1 &3 are modelled at the MTX site of 1d1g, and UNL2 &4 are modelled at the NDP binding site of 1d1g.

    super_omit.png

     Figure 3. Superposition of 394242 (green) with 1d1g (gray). 1sigma omit maps of UNLs are shown.

                    From top to bottom: UNL1 &2 (left), UNL3 &4 (right).


    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags

    Files (3)

    FileSizeDateAttached by 
     asu.png
    No description
    279.64 kB03:14, 16 Sep 2009gyewonActions
     super_omit.png
    No description
    273.59 kB04:13, 2 Oct 2009gyewonActions
     tetramer.png
    No description
    261.35 kB03:14, 16 Sep 2009gyewonActions
    Viewing 1 of 1 comments: view all
    One admits that humen's life seems to be not very cheap, but people require money for different stuff and not every man gets enough cash. Thence to receive quick <a href="http://lowest-rate-loans.com/topics/credit-loans">http://www.lowest-rate-loans.com</a> and collateral loan would be a correct way out.
    Posted 04:49, 28 Jun 2010
    Viewing 1 of 1 comments: view all
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch